Figure 1

Frameshifts cause short alignments with marginal scores. X _i is the ith base of a DNA sequence. Every codon is underscored. is the jth amino acid of a peptide sequence derived under reading frame i. The correct peptide sequence can be derived from the error-free sequence (shown on the top of the figure) under reading frame 1. Because of insertions of two nucleotides (bolded X and Y), the correct peptide sequence is the concatenation of three short peptide sequences derived using different reading frames. Thus, each peptide sequence derived using one reading frame can only generate short alignments with insignificant scores.